Neighboring Clones Research Articles

Abstract SY19-01: Investigating cancer determinants of tumor immune composition

Abstract The cellular composition, spatial architecture, and tissue localization of a tumor have a major impact on a cancer’s progression and response to therapy. These factors are particularly relevant to tumor immunity as immune cell composition and localization within the tumor microenvironment (TME) is one of the major determinants of response to immunotherapy and patient outcome. Spatially resolved single cell genome sequencing has revealed that many genetically distinct sub-clones exist in proximity in tumors and can have different TME compositions, but how specific genes influence the TME, or how neighboring clones influence one another is not well-defined. Indeed, while some genes involved in orchestrating the TME have been identified, the potential roles of many genes in influencing the architecture and immune composition of different tumors are not established. To enable scale up studies to identify determinants of TME biology and tumor immunity, we established a first-of-its-kind in vivo spatial functional genomics platform called Perturb-map. We applied Perturb-map to knockout (KO) dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each KO influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. In contrast to in vitro CRISPR screens, we found KO of positive regulators of IFNγ signaling led to a major reduction of tumor burden, with varying impact from different pathway components. KO of Socs1, a negative regulator of IFNγ signaling, provided a growth advantage though was accompanied by increased T cell infiltration and notably, Socs1 KO tumors were more responsive to PDL1 blockade. Perturb-map also found that KO of the TGFβ Receptor 2 (Tgfbr2) resulted in a growth advantage, but unlike Socs1 KO, T cells were excluded from the lesions and the TME converted to a fibro-mucinous state. Spatial transcriptomics revealed TGFβ signaling was upregulated in Tgfbr2 KO tumors. Further analysis indicated this signal was from TGFβ-mediated activation of fibroblasts in tumors where cancer cells lost Tgfbr2, suggesting the mechanism for TME remodeling and T cell exclusion in Tgfbr2 KO tumors. These studies establish Perturb-map for functional genomics within tissue at single cell-resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME (Dhainaut, Rose et al. BioRxiv 2021, doi.org/10.1101/2021.07.13.451021). Citation Format: Brian Brown. Investigating cancer determinants of tumor immune composition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr SY19-01.

Strategies for the analysis of single-tree plot experiments in Eucalyptus plantations

To verify if the response by Eucalyptus clones in a single-tree plot is influenced by neighboring plants and to determine the effect of missing and/or dominated plants, seven eucalyptus trials in four Brazilian states were analyzed in a randomized complete block design with one plant/plot and 30 replications. Mean annual increment (MAI, m3 ha−1 per year) was determined for three-year-old clones. The influence of neighboring clones was estimated by a linear regression coefficient between the MAI of each clone/plot and the average of a clonal MAI and its eight neighbors. To determine the effect of missing and/or dominated trees, a correction between the MAI and the area available/plant was applied. Subsequent analysis considered unadjusted and adjusted data for missing and dominated trees. Estimate of accuracy and index of coincidence were used to compare the adjustments. In single-tree plots, clone performances were not influenced by neighboring plants. Experimental accuracy was not increased by any of the adjustments employed and the clone ranking was not altered, and therefore did not justify their use.

Randomized, replicated, staggered clonal-row (R2SCR) seed orchard design

Spatial randomization of clones across a seed orchard’s grid is commonly applied to promote cross-fertilization and minimize selfing. The high selection differential attained from advanced-generation breeding programs sets high premier on the genetic gain and diversity delivery from seed orchards, thus clonal allocation is important and even more challenging when clones share common ancestry. Evidences of low selfing in many conifers’ seed orchards, as a result of their high genetic load, inbreeding depression, and polyembryony are abundant and call for orchards’ design re-evaluation, specifically when randomization is associated with added managerial burden. Clonal-rows represent a viable option for simplifying orchards management; however, they are often associated with elevated correlated matings between adjacent clones. Here, we propose a modified clonal-row design that replicates, staggers, and randomizes the rows, thus doubling the number of adjacent clones and providing different set of neighboring clones at each replication, thus allowing accommodating related parents more readily than any single-tree arrangement. We present a novel algorithm packaged in user-friendly software for executing various seed orchards’ designs. The developed program is interactive and suitable for any orchard size and configuration, accommodates any number of clones that are allocated to rows with variable length (ranging from a single tree to any even number) and pre-set separation zone between ramets of the same clone. The program offers three deployment modes (equal, linear, and custom) each with multiple layouts determined by the number of iterations requested. The resulting layouts are ranked based on four criteria including: (1) the number of empty positions, (2) deviation between expected and observed clone size, (3) minimum inbreeding, and (4) a neighborhood index that expresses the efficiency of clonal distribution.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Population dynamics and control of invasiveSpartina alterniflora: inference and forecasting under uncertainty

Managing invaded ecosystems entails making decisions about control strategies in the face of scientific uncertainty and ecological stochasticity. Statistical tools such as model selection and Bayesian decision analysis can guide decision-making by estimating probabilities of outcomes under alternative management scenarios, but these tools have seldom been applied in invasion ecology. We illustrate the use of model selection and Bayesian methods in a case study of smooth cordgrass (Spartina alterniflora) invading Willapa Bay, Washington. To address uncertainty in model structure, we quantified the weight of evidence for two previously proposed hypotheses, that S. alterniflora recruitment varies with climatic conditions (represented by sea surface temperature) and that recruitment is subject to an Allee effect due to pollen limitation. By fitting models to time series data, we found strong support for climate effects, with higher per capita seedling production in warmer years, but no evidence for an Allee effect based on either the total area invaded or the mean distance between neighboring clones. We used the best-supported model to compare alternative control strategies, incorporating uncertainty in parameter estimates and population dynamics. For a fixed annual removal effort, the probability of eradication in 10 years was highest, and final invaded area lowest, if removals targeted the smallest clones rather than the largest or randomly selected clones. The relationship between removal effort and probability of eradication was highly nonlinear, with a sharp threshold separating -0% and -100% probability of success, and this threshold was 95% lower in simulations beginning early rather than late in the invasion. This advantage of a rapid response strategy is due to density-dependent population growth, which produces alternative stable equilibria depending on the initial invasion size when control begins. Our approach could be applied to a wide range of invasive species management problems where appropriate data are available.

Coordination of spermatogenic processes in the testis: lessons from cystic spermatogenesis

A common observation in the vertebrate testis is that new germ cell clones enter spermatogenesis proper before previously formed clones have completed their development. The extent to which the developmental advance of any given germ cell clone in any phase of spermatogenesis is dependent on that of neighboring clones and/or on the coordinating influence of associated Sertoli cells in the immediate vicinity or of others further away remains unclear. This review presents an overall synthesis of findings in an ancient vertebrate, the spiny dogfish shark and shows that, even at this phyletic level, the developmental advance of a given germ cell clone is the outcome of various processes emanating from its spatiotemporal relationship with (1) its own complement of Sertoli cells in the anatomically distinct spermatocyst and (2) Sertoli cells associated with other germ cell clones that lie upstream or downstream in the spermatogenic progression and that secrete, among others, androgen and estrogen destined for target sites upstream. Analysis of the protracted spermatogenic cycle shows the coordination in space and time of spermatogenic and steroidogenic events. Furthermore, the natural withdrawal of pituitary gonadotropin support in the dogfish causes a distinct and highly ordered gradient of apoptosis among the spermatogonial generations; this in turn is a major contributing factor to the cyclic nature of sperm production observed in this lower vertebrate. Because of the simplicity of their testicular organization, their cystic spermatogenesis and their phylogenetic position, cartilaginous fishes constitute a valid vertebrate reference system for comparative analysis with higher vertebrates.

Identification of Differential Aberrations in Multiple-Sample Array CGH Studies

Most existing methods for identifying aberrant regions with array CGH data are confined to a single target sample. Focusing on the comparison of multiple samples from two different groups, we develop a new penalized regression approach with a fused adaptive lasso penalty to accommodate the spatial dependence of the clones. The nonrandom aberrant genomic segments are determined by assessing the significance of the differences between neighboring clones and neighboring segments. The algorithm proposed in this article is a first attempt to simultaneously detect the common aberrant regions within each group, and the regions where the two groups differ in copy number changes. The simulation study suggests that the proposed procedure outperforms the commonly used single-sample aberration detection methods for segmentation in terms of both false positives and false negatives. To further assess the value of the proposed method, we analyze a data set from a study that identified the aberrant genomic regions associated with grade subgroups of breast cancer tumors.

Analysis of array CGH data for cancer studies using fused quantile regression

The identification of DNA copy number changes provides insights that may advance our understanding of initiation and progression of cancer. Array-based comparative genomic hybridization (array-CGH) has emerged as a technique allowing high-throughput genome-wide scanning for chromosomal aberrations. A number of statistical methods have been proposed for the analysis of array-CGH data. In this article, we consider a fused quantile regression model based on three motivations: (1) quantile regression may provide a more comprehensive picture for the ratio profile of copy numbers than the standard mean regression approach; (2) for simplicity, most available methods assume uniform spacing between neighboring clones, while incorporating the information of physical locations of clones may be helpful and (3) most current methods have a set of tuning parameters that must be carefully tuned, which introduces complexity to the implementation. We formulate the detection of regions of gains and losses in a fused regularized quantile regression framework, incorporating physical locations of clones. We derive an efficient algorithm that computes the entire solution path for the resulting optimization problem, and we propose a simple estimate for the complexity of the fitted model, which leads to convenient selection of the tuning parameter. Three published array-CGH datasets are used to demonstrate our approach. R code are available at http://www.stat.lsa.umich.edu/~jizhu/code/cgh/. Supplementary data are available at Bioinformatics online.

CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss

An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R.

No Evidence For Large-scale Germline Genomic Aberrations in Hereditary Bladder Cancer Patients with High-Resolution Array-Based Comparative Genomic Hybridization

Linkage studies in high-risk families have led to the identification of several important susceptibility genes for hereditary cancer. Unfortunately, such studies offer limited possibilities in the search for high-penetrance bladder cancer genes, as extended bladder cancer families are very rare.

Competitive equivalence maintains persistent inter-clonal boundaries

Clear boundaries often separate adjacent conspecific competitors. These boundaries may reflect bordering animal territories or regions of inter-organism contact in mobile and non-mobile organisms, respectively. Sessile, clonal organisms often form persistent inter-clonal boundaries despite great variation in competitive ability among genotypes within a population. I show that neighboring clones in the sea anemone Anthopleura elegantissima and three species of the marine hydroid genus Hydractinia are more evenly matched in terms of competitive ability than expected by chance. Hypotheses of genetic relatedness or similar environmental regime shared by neighboring clones are inconsistent with the observed similarities between adjacent competitors in one or both taxa. Instead, inter-clonal borders evidently persist as standoffs between evenly matched competitors. Large differences in competitive ability between bordering clones were rarely observed, suggesting that dominant clones quickly displace or eliminate others in competitive mismatches. This ecological parallel between taxa (i.e., competitive equivalence) exists despite several fundamental differences (e.g., geographical distribution, habitat, body size, longevity), suggesting that competitive equivalence may be a widespread determinant of boundary persistence between adjacent competitors.

Can germplasm resources be used to increase the ascorbic acid content of stored potatoes?

Freshly harvested potato tubers contain up to 50 mg/100g ascorbic acid (AA), but levels decline rapidly during cold storage. Genetic alterations to boost the AA content of stored tubers would contribute to human nutrition and might improve tuber resistance to oxidative damage during chilling. While studying the breeding potential ofSolanum phureja germplasm, we identified a 24-chromosome Phureja-haploid Tuberosum hybrid (clone I, USW5295.7) that retained a twofold higher content of tuber AA than neighboring clones after storage at 5 C. Clone I produces 2n-pollen through a mechanism genetically equivalent to first-division restitution (FDR), which transmits much of the nonadditive genetic variance for tuber yield. We now report a survey of clone I progeny showing significant family and ploidy effects on tuber AA levels during cold storage, consistent with the transmission of information for higher AA by FDR 2n-pollen. These results encourage further study of 2n-gametes and wild species germplasm to breed for increased tuber AA.

A New Method to Assess Competition in Coffee Clonal Trials with Single‐Tree Plots in Côte d'Ivoire

A new method is proposed for the assessment of competition in clonal trials with completely randomized single‐tree plots, without needing to choose a covariable a priori linked to competition. This method is applied to a coffee clonal trial planted in a completely randomized single‐tree plot design located in Côte d'Ivoire. Microenvironmental effects were first taken into account using the conventional Papadakis method. The competition effect (Ck) of each clone (k) was then estimated as the influence of its presence on the residual value, after removal of the clonal effect, of its neighbors. Residuals were thus modeled as a linear regression of the neighboring clones’ C value. Competition effects were shown this way to explain 4% of the residual yield in young trees and 10% in adult trees. Several clones had C values significantly different from 0. Some were identified as aggressive for their neighbors (C < 0), others as stimulating (i.e., promoting yield, C > 0). Architecture and vigor variables that were likely to be related to the C value of clones were then sought. For young trees, vigor, estimated by stem diameter, was best correlated to competition effects: vigorous clones were more aggressive than others. When trees became adult, the length of the orthotropic internodes (Lort) was the trait that most effectively explained (42%) the competition effect of clones: the shorter the internodes, the less aggressive was the clone. In the future, Lort may thus be used in a selection index to prevent from selecting aggressive coffee clones that would undergo their own aggressiveness when grown alone in plantations.

Leech Segmental Repeats Develop Normally in the Absence of Signals from either Anterior or Posterior Segments

We have investigated whether the development of segmental repeats is autonomous in the embryo of the leech Helobdella robusta. The segmental tissues of the germinal band arise from progeny of five stem cells called teloblasts. Asymmetric divisions of the teloblasts form chains of segment founder cells (called primary blast cells) that divide in a stereotypical manner to produce differentiated descendants. Using two distinct techniques, we have looked for potential interactions between neighboring blast cell clones along the anterior–posterior axis. In one technique, we prevented the birth of primary blast cells by injection of DNase I into the teloblast, thereby depriving the last blast cell produced before the ablation of its normal posterior neighbors. We also ablated single blast cells with a laser microbeam, which allowed us to assess potential signals acting on either more anterior or more posterior primary blast cell clones. Our results suggest that interactions along the anterior–posterior axis between neighboring primary blast cell clones are not required for development of normal segmental organization within the blast cell clone. We also examined the possibility that blast cells receive redundant signals from both anterior and posterior neighboring clones and that either is sufficient for normal development. Using double blast cell laser ablations to isolate a primary blast cell clone by removal of both its anterior and its posterior neighbor, we found that the isolated clone still develops normally. These results reveal that the fundamental segmental repeat in the leech embryo, the primary blast cell clone, can develop normally in the apparent absence of signals from adjacent repeats along the anterior–posterior axis.

ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling.

In the program ODS_BOOTSTRAP we provide a methodology for quickly ordering clones in a genomic library into a physical map and for applying a statistical tool known as the bootstrap to assess the statistical reliability of a clonal ordering. Each clone is assigned a binary fingerprint by one of a variety of experimental approaches to physical mapping. For example, the binary fingerprints might be generated by hybridizing a panel of m probes to a library of n clones. The resulting n x m binary data matrix, X, is input to ODS_BOOTSTRAP, which utilizes the similarity in binary fingerprints of clones to construct a physical map. Under this particular implementation of bootstrap resampling, the m probes (or columns of the data matrix) are sampled randomly with replacement in the computer to generate a new n x m data matrix, X*, from which a second physical map is constructed. The resampling process is repeated 100 or more times to generate 100 or more X* matrices. The resulting 100 or more physical maps are compared with the original physical map based on the original data matrix X by counting how often links in the original physical map reappear. Three confidence statistics are introduced for each link in a physical map. The statistic C1 is defined as the percentage of time two neighboring clones on the original map reappear as neighbors under resampling. The statistic C2 is defined as the percentage of time that two neighboring clones i and j on the original map reappear as neighbors or that a clone with an identical binary fingerprint to clone i reappears as a neighbor to clone j. The statistic C3 is defined as the percentage of time that two neighboring clones on the original map reappear in the same contig under resampling.

A Chromosome 11 YAC Library

A targeted yeast artificial chromosome (YAC) library for chromosome 11 has been constructed from the J1 cell line that carries a single human chromosome 11 within a hamster DNA background. Interspecies chimeric clones generated during construction of the library were detected during the screening process and eliminated from the library. Contig assembly becomes much less difficult using such a library as the complexity is decreased and the ends of the clone inserts can be rescued far walking to neighboring clones. The library contains > 1824 clones with an average insert length of 337 kb. This represents a fourfold coverage of chromosome 11 or a > 95% chance of recovering a unique single-copy sequence from the library. Two hundred YAC clones were localized by fluorescence in situ hybridization and found to be randomly distributed along the chromosome. The library has been screened with probes for the chromosome 11 markers HBB, GLUR4, H19, and D11S193. Corresponding YAC clones have been isolated for each locus. This analysis has indicated that the library is unbiased, that cognate YAC clones can be recovered with chromosome 11 markers, and that extensive contig assembly should be feasible.

Fruit and seed set in Mayapple (Podophyllum peltatum): influence of intraspecific factors and local enhancement near Pedicularis canadensis

The breeding system and determinants of fruit and seed production in a population of 114 patches of Mayapple (Podophyllum peltatum L.) were examined. Experimental crosses indicated that Mayapple patches are self-incompatible (clones) and that fruit and seed set were pollinator limited. Mayapple flowers are nectarless yet depend primarily on infrequent visits by nectar-searching bumblebees for pollination. The proportion of flowers setting fruit and ovules setting seed in Mayapple clones was inversely associated with the distance to neighboring clones and the distance to Pedicularis canadensis L. plants. Clones within 45 m of P. canadensis plants (which are heavily visited by bumblebees) showed significant increases in fruit and seed production compared with a similar group of more distant clones. This effect is interpreted as evidence for a facilitative interaction between Mayapple and P. canadensis.